This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see http://rmarkdown.rstudio.com.
When you click the Knit button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:
summary(cars)
## speed dist
## Min. : 4.0 Min. : 2.00
## 1st Qu.:12.0 1st Qu.: 26.00
## Median :15.0 Median : 36.00
## Mean :15.4 Mean : 42.98
## 3rd Qu.:19.0 3rd Qu.: 56.00
## Max. :25.0 Max. :120.00
library('ggplot2')
library('plotly')
##
## Attaching package: 'plotly'
## The following object is masked from 'package:ggplot2':
##
## last_plot
## The following object is masked from 'package:stats':
##
## filter
## The following object is masked from 'package:graphics':
##
## layout
setwd('~/mygraph2/bin/')
mygenes <- read.csv('gene_dist_head.tsv', header= TRUE, sep = "\t",fill = TRUE)
autosomes<-c("1","2","3","4","5","6","7","8","9","10",
"11","12","13","14","15","16","17","18","19","20","21","22")
genes<- mygenes[ which(mygenes$chr %in% autosomes), ]
genes$chr <- factor(genes$chr, levels = autosomes)
ggplot(data = genes) + geom_bar(mapping = aes(x = chr, fill = feature), width = 1)
ggplot(data = genes) +
geom_bar(mapping = aes(x = chr, fill = feature), width = 1) +
coord_polar()
p<-ggplot(data = genes) +
geom_bar(mapping = aes(x = chr, fill = feature), width = 1)
ggplotly(p)
You can also embed plots, for example:
Note that the echo = FALSE parameter was added to the code chunk to prevent printing of the R code that generated the plot.